Partial base flipping is sufficient for strand slippage near DNA duplex termini

Journal of the American Chemical Society

Volumn 135, Issue 22, 2013, Pages 8274-8282

  Banavali, Nilesh K ^a,b  

^a WADSWORTH CENTER   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLOSE RELATIONSHIPS; DELETION MUTATIONS; FLIPPING MECHANISMS; METASTABLE INTERMEDIATE; MOLECULAR DYNAMICS SIMULATIONS; POLYMERASE ACTIVE SITE; STRUCTURAL DISTORTIONS; STRUCTURAL MECHANISMS;

MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; POLYMERS;

DNA;

CYTOSINE; DNA POLYMERASE; DOUBLE STRANDED DNA; GUANINE; NUCLEIC ACID;

ARTICLE; ATOM; DELETION MUTANT; DNA SEQUENCE; DNA STRAND BREAKAGE; DNA STRUCTURE; MOLECULAR DYNAMICS; MUTATION; TERMINAL SEQUENCE;

BASE SEQUENCE; DNA; MOLECULAR DYNAMICS SIMULATION;

EID: 84878623724     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja401573j     Document Type: Article

References (68)

1. Garcia-Diaz, M.; Kunkel, T. Trends Biochem. Sci. 2006, 31, 206-214
2. Kunkel, T. J. Biol. Chem. 2004, 279, 16895-16898
3. Streisinger, G.; Okada, Y.; Emrich, J.; Newton, J.; Tsugita, A.; Terzaghi, E.; Inouye, M. Frameshift mutations and the genetic code. In Cold Spring Harbor Symposia on Quantitative Biology, Vol. 31; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1966.
4. Kunkel, T.; Soni, A. J. Biol. Chem. 1988, 263, 14784-14789
5. Fujii, S.; Akiyama, M.; Aoki, K.; Sugaya, Y.; Higuchi, K.; Hiraoka, M.; Miki, Y.; Saitoh, N.; Yoshiyama, K.; Ihara, K.; Seki, M.; Ohtsubo, E.; Maki, H. J. Mol. Biol. 1999, 289, 835-850
6. Kunkel, T. J. Biol. Chem. 1986, 261, 13581-13587
7. Efrati, E.; Tocco, G.; Eritja, R.; Wilson, S.; Goodman, M. J. Biol. Chem. 1997, 272, 2559-2569
8. Ling, H.; Boudsocq, F.; Woodgate, R.; Yang, W. Cell 2001, 107, 91-102
9. Garcia-Diaz, M.; Bebenek, K.; Krahn, J.; Pedersen, L.; Kunkel, T. Cell 2006, 124, 331-342
10. Wilson, R.; Pata, J. Mol. Cell 2008, 29, 767-779
11. Ling, H.; Boudsocq, F.; Woodgate, R.; Yang, W. Mol. Cell 2004, 13, 751-762
12. Zhang, H.; Eoff, R.; Kozekov, I.; Rizzo, C.; Egli, M.; Guengerich, F. J. Biol. Chem. 2009, 284, 3563-3576
13. DeLucia, A.; Grindley, N.; Joyce, C. Biochemistry 2007, 46, 10790-10803
14. Woodson, S.; Crothers, D. Biochemistry 1987, 26, 904-912
15. Woodson, S.; Crothers, D. Biochemistry 1988, 27, 436-445
16. Weisenseel, J.; Moe, J.; Reddy, G.; Marnett, L.; Stone, M. Biochemistry 1995, 34, 50-64
17. Wang, Y.; Schnetz-Boutaud, N.; Saleh, S.; Marnett, L.; Stone, M. Chem. Res. Toxicol. 2007, 20, 1200-1210
18. Chi, L.; Lam, S. FEBS Lett. 2006, 580, 6496-6500
19. Chi, L.; Lam, S. Biochemistry 2007, 46, 9292-9300
20. Chi, L.; Lam, S. Biochemistry 2008, 47, 4469-4476
21. Chi, L.; Lam, S. Biochemistry 2009, 48, 11478-11486
22. Chi, L.; Lam, S. J. Phys. Chem. B 2012, 116, 1999-2007
23. Foloppe, N.; Gueroult, M.; Hartmann, B. Methods Mol. Biol. (Clifton, NJ) 2013, 924, 445-468
24. Liu, L.; Bradley, P. Curr. Opin. Struct. Biol. 2012, 22, 397-405
25. Konrad, M.; Bolonick, J. J. Am. Chem. Soc. 1996, 118, 10989-10994
26. Lebrun, A.; Lavery, R. J. Biomol. Struct. Dyn. 1998, 16, 593-604
27. MacKerell, A., Jr.; Lee, G. Eur. Biophys. J. 1999, 28, 415-426
28. Yang, L.; Beard, W.; Wilson, S.; Roux, B.; Broyde, S.; Schlick, T. J. Mol. Biol. 2002, 321, 459-478
29. Bebenek, K.; Garcia-Diaz, M.; Foley, M.; Pedersen, L.; Schlick, T.; Kunkel, T. EMBO Rep. 2008, 9, 459-464
30. Mura, C.; McCammon, J. Nucleic Acids Res. 2008, 36, 4941-4955
31. Foley, M.; Padow, V.; Schlick, T. J. Am. Chem. Soc. 2010, 132, 13403
32. Xu, P.; Oum, L.; Geacintov, N.; Broyde, S. Biochemistry 2008, 47, 2701-2709
33. Potapova, O.; Grindley, N.; Joyce, C. J. Biol. Chem. 2002, 277, 28157-28166
34. Banavali, N.; MacKerell, A. J. Mol. Biol. 2002, 319, 141-160
35. Varnai, P.; Lavery, R. J. Am. Chem. Soc. 2002, 124, 7272-7273
36. Huang, N.; Banavali, N.; MacKerell, A., Jr. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 68-73
37. Giudice, E.; Varnai, P.; Lavery, R. Nucleic Acids Res. 2003, 31, 1434-1443
38. Banavali, N.; MacKerell, A. PLoS One 2009, 4, e5525
39. Leontis, N.; Westhof, E. Q. Rev. Biophys. 1998, 31, 399-455
40. Leontis, N.; Westhof, E. RNA 2001, 7, 499-512
41. Ban, N.; Nissen, P.; Hansen, J.; Moore, P.; Steitz, T. Science 2000, 289, 905-920
42. Foloppe, N.; MacKerell, A., Jr. J. Comput. Chem. 2000, 21, 86-104
43. MacKerell, A.; Banavali, N. J. Comput. Chem. 2000, 21, 105-120
44. Cornell, W.; Cieplak, P.; Bayly, C.; Gould, I.; Merz, K.; Ferguson, D.; Spellmeyer, D.; Fox, T.; Caldwell, J.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179-5197
45. Cheatham, T., III; Cieplak, P.; Kollman, P. J. Biomol. Struct. Dyn. 1999, 16, 845-862
46. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T., III; Laughton, C.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
47. Langley, D. J. Biomol. Struct. Dyn. 1998, 16, 487-509
48. Hart, K.; Foloppe, N.; Baker, C. M.; Denning, E. J.; Nilsson, L.; MacKerell, A. D., Jr. J. Chem. Theory Comput. 2011, 8, 348-362
49. Banavali, N.; Roux, B. J. Am. Chem. Soc. 2005, 127, 6866-6876
50. Shea, J.; Onuchic, J.; Brooks, C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16064-16068
51. Yang, S.; Banavali, N. K.; Roux, B. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 3776-3781
52. Xia, S.; Konigsberg, W.; Wang, J. J. Am. Chem. Soc. 2011, 133, 10003-10005
53. Sarver, M.; Zirbel, C. L.; Stombaugh, J.; Mokdad, A.; Leontis, N. B. J. Math. Biol. 2008, 56, 215-252
54. Brooks, B.; Bruccoleri, R.; Olafson, B.; Swaminathan, S.; Kar plus, M. J. Comput. Chem. 1983, 4, 187-217
55. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614
56. Nelson, M. T.; Humphrey, W.; Gursoy, A.; Dalke, A.; Kaĺ e, L. V.; Skeel, R. D.; Schulten, K. Int. J. High Perf. Comput. Appl. 1996, 10, 251-268
57. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
58. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem. Phys. 1983, 79, 926
59. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050-9063
60. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
61. Feller, S.; Zhang, Y.; Pastor, R.; Brooks, B. J. Chem. Phys. 1995, 103, 4613-4621
62. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
63. Sayle, R.; Milner-White, E. Trends Biochem. Sci. 1995, 20, 374
64. Kabsch, W. Acta Crystallogr. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 1978, 34, 827-828
65. Bolhuis, P.; Chandler, D.; Dellago, C.; Geissler, P. Annu. Rev. Phys. Chem. 2002, 53, 291-318
66. Weinan, E.; Ren, W.; Vanden-Eijnden, E. Phys. Rev. B 2002, 66, 052301
67. Weinan, E.; Ren, W.; Vanden-Eijnden, E. J. Chem. Phys. 2007, 126, 164103
68. Hart, K.; Nystrom, B.; Ohman, M.; Nilsson, L. RNA 2005, 11, 609-618